☰ Navigation Tabs
TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo-TssM; individual search models for Ig-like and catalytic domain; Ig-like domain had its b1 strand removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.06 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.75 α = 90 b = 103.75 β = 90 c = 191.52 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M default 2021-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.62 103.74 99.9 0.076 0.08 0.9990000000000001 18.54 13.42 132701
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.66 2.335 2.425 0.516 1.19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.62 91.22 130701 2000 99.95 0.17473 0.17436 0.1846 0.19822 0.2035 RANDOM 28.719
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.47 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.039 r_dihedral_angle_2_deg 10.686 r_long_range_B_refined 8.062 r_long_range_B_other 8.013 r_scangle_other 6.612 r_dihedral_angle_1_deg 6.267 r_scbond_it 4.536 r_scbond_other 4.536 r_mcangle_it 3.787 r_mcangle_other 3.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.039 r_dihedral_angle_2_deg 10.686 r_long_range_B_refined 8.062 r_long_range_B_other 8.013 r_scangle_other 6.612 r_dihedral_angle_1_deg 6.267 r_scbond_it 4.536 r_scbond_other 4.536 r_mcangle_it 3.787 r_mcangle_other 3.787 r_mcbond_it 2.789 r_mcbond_other 2.789 r_angle_refined_deg 1.76 r_angle_other_deg 0.579 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5704 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing